Liphardt Lab


We're a team of physicists, engineers, and biologists. We investigate the organization and dynamics of single molecules in living cells. We also develop optical and statistical tools for collecting large amounts of data and then using this information to find underlying organizational principles. Our lab is located in the Shriram Center.

Beyond biophysics, we are also interested to tackle problems in medicine. To help bring together patients, engineers, and social networking technologists, and to create larger training sets for artificial intelligence and machine learning, we recently co-founded CancerBase, a place where patients can share medical data and learn from one-another. We think of CancerBase as an early example for how the internet and cryptography can help reshape healthcare in the US and elsewhere.



Major Research Directions: Patterns, Energy, and Information


Nucleus

Genome-wide coordination of gene expression

Imagine you are an orchestra conductor directing a symphony. If you're good at what you do, everything will sound right. How does the genome solve the equivalent problem, except without a conductor? We use genome-edited cell lines to investigate how DNA-looping and chromatin compaction influence transcriptional regulation. The image above shows a single nucleus. The DNA is blue, single RNA transcripts are red/yellow.

Data

Data analysis

We use concepts and tools from non-equilibrium statistical mechanics, polymer physics, and gelation to model and explore biological processes, such as how chromatin is organized and how it moves inside the cell nucleus.

NPC

Single molecule studies of the Nuclear Pore Complex

In collaboration with Karsten Weis, we are using single-molecule tracking approaches to learn how the NPC controls access to the nucleus. The image shows a schematic of a NPC in the nuclear membrane, and a single cargo transiting the pore. The panel below shows a single cargo being tracked as it translocates the pore. The NPC is both highly selective and efficient; our goal is to understand how the pore implements those apparently conflicting goals. Moreover, we would like to clarify the fundamental basis for the pore's ability to efficiently rectify molecular transport.



Tools for Control and Measurement; Polymers and Forces


Rotating E. coli

Plasmon Rulers

RNA

Nanowires

DNA Loops

Tools and methods. Scroll over the images to learn more.